The Regulatory Genome

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Author: Eric H. Davidson
Publisher: Elsevier
ISBN: 9780080455570
Size: 52.20 MB
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The Regulatory Genome by Eric H. Davidson


Original Title: The Regulatory Genome

Gene regulatory networks are the most complex, extensive control systems found in nature. The interaction between biology and evolution has been the subject of great interest in recent years. The author, Eric Davidson, has been instrumental in elucidating this relationship. He is a world renowned scientist and a major contributor to the field of developmental biology. The Regulatory Genome beautifully explains the control of animal development in terms of structure/function relations of inherited regulatory DNA sequence, and the emergent properties of the gene regulatory networks composed of these sequences. New insights into the mechanisms of body plan evolution are derived from considerations of the consequences of change in developmental gene regulatory networks. Examples of crucial evidence underscore each major concept. The clear writing style explains regulatory causality without requiring a sophisticated background in descriptive developmental biology. This unique text supersedes anything currently available in the market. The only book in the market that is solely devoted to the genomic regulatory code for animal development Written at a conceptual level, including many novel synthetic concepts that ultimately simplify understanding Presents a comprehensive treatment of molecular control elements that determine the function of genes Provides a comparative treatment of development, based on principles rather than description of developmental processes Considers the evolutionary processes in terms of the structural properties of gene regulatory networks Includes 42 full-color descriptive figures and diagrams

Regulatory Genomics

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Author: Leong Hon Wai
Publisher: World Scientific
ISBN: 1908978740
Size: 19.51 MB
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Regulatory Genomics by Leong Hon Wai


Original Title: Regulatory Genomics

Research in the field of gene regulation is evolving rapidly in the ever-changing scientific environment. Advances in microarray techniques and comparative genomics have enabled more comprehensive studies of regulatory genomics. The study of genomic binding locations of transcription factors has enabled a more comprehensive modeling of regulatory networks. In addition, complete genomic sequences and comparison of numerous related species have demonstrated the conservation of non-coding DNA sequences, which often provide evidence for cis-regulatory binding sites. Systematic methods to decipher the regulatory mechanism are also crucial for corroborating these regulatory networks; key to these methods are motif discovery algorithms that can help predict cis-regulatory elements. These DNA-motif discovery programs are becoming more sophisticated and are beginning to leverage evidence from comparative genomics. These topics and more were discussed at the 3rd Annual RECOMB Workshop on Regulatory Genomics, which brought together more than 90 attendees and included about 22 excellent talks from leading researchers in the field. This proceedings volume contains ten selected, original manuscripts that were presented during the workshop. Contents:TScan: A Two-step De Novo Motif Discovery Method (O Abul et al.)Redundancy Elimination in Motif Discovery Algorithms (H Leung & F Chin)GAMOT: An Efficient Genetic Algorithm for Finding Challenging Motifs in DNA Sequences (N Karaoglu et al.)Identification of Spaced Regulatory Sites via Submotif Modeling (E Wijaya & R Kanagasabai)Refining Motif Finders with E-value Calculations (N Nagarajan et al.)Multiple Indexing Sequence Alignment for Group Feature Identification (W-Y Chou et al.)Improving the Accuracy of Signal Transduction Pathway Construction Using Level-2 Neighbours (T K F Wong et al.)Investigating Roles of DNA Flexibility in Promoter Recognition and Regulation (J D Bashford)Regulatory Networks of Genes Affected by MorA, A Global Regulator Containing GGDEF and EAL Domains in Pseudomonas Aeruginosa (W-K Choy et al.)and other papers Readership: Graduate, postgraduate and research academics as well as professionals in the area of gene regulation. Keywords:Bioinformatics;Computational Biology;Gene Regulation;Genemoic;Regulatory Genomics;Transcription FactorsKey Features:Contains the latest research results in regulatory genomics by experts in this area

Systems Biology And Regulatory Genomics

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Author: Eleazar Eskin
Publisher: Springer Science & Business Media
ISBN: 3540482938
Size: 71.66 MB
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Systems Biology And Regulatory Genomics by Eleazar Eskin


Original Title: Systems Biology And Regulatory Genomics

This book constitutes the thoroughly refereed post-proceedings of two joint RECOMB 2005 satellite events: the First Annual Workshop on Systems Biology, RSB 2005 and the Second Annual Workshop on Regulatory Genomics, RRG 2005, held in San Diego, CA, USA in December 2005. It contains 21 revised full papers that address a broad variety of topics in systems biology and regulatory genomics.

Genomic Control Process

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Author: Isabelle Peter
Publisher: Academic Press
ISBN: 0124047467
Size: 62.52 MB
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Genomic Control Process by Isabelle Peter


Original Title: Genomic Control Process

Genomic Control Process explores the biological phenomena around genomic regulatory systems that control and shape animal development processes, and which determine the nature of evolutionary processes that affect body plan. Unifying and simplifying the descriptions of development and evolution by focusing on the causality in these processes, it provides a comprehensive method of considering genomic control across diverse biological processes. This book is essential for graduate researchers in genomics, systems biology and molecular biology seeking to understand deep biological processes which regulate the structure of animals during development. Covers a vast area of current biological research to produce a genome oriented regulatory bioscience of animal life Places gene regulation, embryonic and postembryonic development, and evolution of the body plan in a unified conceptual framework Provides the conceptual keys to interpret a broad developmental and evolutionary landscape with precise experimental illustrations drawn from contemporary literature Includes a range of material, from developmental phenomenology to quantitative and logic models, from phylogenetics to the molecular biology of gene regulation, from animal models of all kinds to evidence of every relevant type Demonstrates the causal power of system-level understanding of genomic control process Conceptually organizes a constellation of complex and diverse biological phenomena Investigates fundamental developmental control system logic in diverse circumstances and expresses these in conceptual models Explores mechanistic evolutionary processes, illuminating the evolutionary consequences of developmental control systems as they are encoded in the genome

Regulatory Genomics

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Author: Bogdan Tanasa
Publisher:
ISBN: 9781303457241
Size: 38.67 MB
Format: PDF
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Regulatory Genomics by Bogdan Tanasa


Original Title: Regulatory Genomics

In the present dissertation, I integrate contemporary high-throughput sequencing (HT-seq) methods to characterize regulatory elements and transcriptional units in several biological systems in order to understand the molecular networks regulating the processes of gene expression. Our intense efforts contributed to several discoveries in biology, including a. the discovery of novel small RNA species that regulate mRNAs stability - the riRNAs, b. finding novel transcriptional units that regulate estrogen-dependent transcriptional events - the eRNAs, c. establishing the role of long noncoding RNAs in androgen-dependent gene expression - the lincRNAs PCGEM1 and PRNCR1, d. elucidating a novel epigenomics regulator - PHF8 as a H4K20me1 demethylase, e. characterizing a multifaceted transcrip- tional regulator - GPS2, f. identifying novel GWAS loci located in enhancers that carry disease susceptibility alleles. Chapter 1 reviews the current knowledge on genome regulatory elements, transcriptional units and chromatin architecture, and it describes 8 computational protocols that I have established in the laboratory for data analysis, together with their biological applications and methodological limitations. Chapter 2 details the use of HT-seq methods to characterize 2 novel transcriptional regulators (PHF8 and GPS2 ) that associate with promoters. Chapter 3 describes a novel small RNA species (riRNAs ), that derives from Alu retrotransposons and was bioin- formatically predicted to target the mRNAs. Chapter 4 describes the functions of enhancer RNAs in gene expression and chromatin interactions, by employ- ing GRO-seq and 3D-DSL methods. Chapter 5 describes 2 lincRNAs (PRNCR1, PCGEM1 ) that are over-expressed in prostate cancers and regulate tumor growth, by using ChIRP-seq and GRO-seq methods. Chapter 6 describes the biological functions of an enhancer in 9p21 gene desert, that carries genetic susceptibility to disease, and advances in 3D-DSL technology. I conclude with a section that summarizes these discoveries and outlines the potential areas of future research.

Genomic Control Process

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Author: Isabelle Peter
Publisher: Academic Press
ISBN: 0124047467
Size: 41.91 MB
Format: PDF, ePub, Docs
View: 3999

Genomic Control Process by Isabelle Peter


Original Title: Genomic Control Process

Genomic Control Process explores the biological phenomena around genomic regulatory systems that control and shape animal development processes, and which determine the nature of evolutionary processes that affect body plan. Unifying and simplifying the descriptions of development and evolution by focusing on the causality in these processes, it provides a comprehensive method of considering genomic control across diverse biological processes. This book is essential for graduate researchers in genomics, systems biology and molecular biology seeking to understand deep biological processes which regulate the structure of animals during development. Covers a vast area of current biological research to produce a genome oriented regulatory bioscience of animal life Places gene regulation, embryonic and postembryonic development, and evolution of the body plan in a unified conceptual framework Provides the conceptual keys to interpret a broad developmental and evolutionary landscape with precise experimental illustrations drawn from contemporary literature Includes a range of material, from developmental phenomenology to quantitative and logic models, from phylogenetics to the molecular biology of gene regulation, from animal models of all kinds to evidence of every relevant type Demonstrates the causal power of system-level understanding of genomic control process Conceptually organizes a constellation of complex and diverse biological phenomena Investigates fundamental developmental control system logic in diverse circumstances and expresses these in conceptual models Explores mechanistic evolutionary processes, illuminating the evolutionary consequences of developmental control systems as they are encoded in the genome

Introduction To Genomics

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Author: Arthur Lesk
Publisher: Oxford University Press
ISBN: 0199564353
Size: 54.73 MB
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Introduction To Genomics by Arthur Lesk


Original Title: Introduction To Genomics

Our genome is the blueprint to our existence: it encodes all the information we need to develop from a single cell into a hugely complicated functional organism. But how do we identify the genes that make up our genome? How do we determine their function? And how do different genes form the regulatory networks that direct the processes of life? Introduction to Genomics is a fascinating insight into what can be revealed from the study of genomes: how organisms differ or match; how different organisms evolved; how the genome is constructed and how it operates; and what our understanding of genome structure and function means in terms of our future health and wellbeing. Thoroughly revised and brought up to date, the second edition features: * Coverage of the latest techniques and developments in the field * Rich pedagogy: End-of-chapter exercises, web-based problems ("weblems"), and lab assignments; "Special Topic" boxes; engaging case studies new "Ethics" boxes exploring the ethical issues surrounding the study of genomics; highlighted key terms; and an end-of-book glossary * A larger format provides greater clarity to the text and accompanying figures * Five new chapters, including one dedicated to metabolomics * An updated Companion Website (www.oup.com/uk/orc/bin/9780199564354) offering a range of resources, including figures from the book in electronic format, answers to end-of-chapter exercises, hints to end-of-chapter problems, a guided tour of web sites in genomics, and rotating figures The field of genomics is enabling us to analyze life in more detail than ever before; and Introduction to Genomics tackles this conceptually challenging--and fascinating--subject in a clear, lucid way.

Animal Evolution

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Author: Maximilian J. Telford
Publisher: Oxford University Press
ISBN: 0199549427
Size: 58.72 MB
Format: PDF
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Animal Evolution by Maximilian J. Telford


Original Title: Animal Evolution

Describing and understanding the evolution of the diversity of bodyplans is a major goal of evolutionary biology. Taking a modern, integrated approach to this question, a group of leading researchers describe how modern techniques and disciplines have been combined, resulting in a dramatic renaissance in the study of animal evolution.

Clinical Genomics

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Author: Shashikant Kulkarni
Publisher: Academic Press
ISBN: 0124051731
Size: 24.69 MB
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Clinical Genomics by Shashikant Kulkarni


Original Title: Clinical Genomics

Clinical Genomics provides an overview of the various next-generation sequencing (NGS) technologies that are currently used in clinical diagnostic laboratories. It presents key bioinformatic challenges and the solutions that must be addressed by clinical genomicists and genomic pathologists, such as specific pipelines for identification of the full range of variants that are clinically important. This book is also focused on the challenges of diagnostic interpretation of NGS results in a clinical setting. Its final sections are devoted to the emerging regulatory issues that will govern clinical use of NGS, and reimbursement paradigms that will affect the way in which laboratory professionals get paid for the testing. Simplifies complexities of NGS technologies for rapid education of clinical genomicists and genomic pathologists towards genomic medicine paradigm Tried and tested practice-based analysis for precision diagnosis and treatment plans Specific pipelines and meta-analysis for full range of clinically important variants

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